Grantee Research Project Results
2020 Progress Report: Cardiotoxicity Adverse Outcome Pathway: Organotypic Culture Model and in vitro-to-in vivo Extrapolation for High-throughput Hazard, Dose-response and Variability Assessments
EPA Grant Number: R835802Center: Organotypic Culture Models For Predictive Toxicology Center
Center Director: Rusyn, Ivan
Title: Cardiotoxicity Adverse Outcome Pathway: Organotypic Culture Model and in vitro-to-in vivo Extrapolation for High-throughput Hazard, Dose-response and Variability Assessments
Investigators: Rusyn, Ivan , Wright, Fred A. , Threadgill, David W.
Current Investigators: Rusyn, Ivan
Institution: Texas A & M University , North Carolina State University , The Hamner Institutes
Current Institution: Texas A & M University , North Carolina State University
EPA Project Officer: Callan, Richard
Project Period: June 1, 2015 through May 31, 2019 (Extended to May 31, 2022)
Project Period Covered by this Report: June 1, 2020 through May 31,2021
Project Amount: $6,000,000
RFA: Organotypic Culture Models for Predictive Toxicology Center (2013) RFA Text | Recipients Lists
Research Category: Chemical Safety for Sustainability
Progress Summary:
Project 1 work was focused on using multi-plexed assays for high-content imaging and high-throughput transcriptomic analyses using human iCell cardiomyocyte organotypic culture model and other cell types derived from iPS cells. We are analyzing the data from testing 140 compounds selected in consultation with FDA, NTP and EPA-NCCT in a population-based in vitro iPSC-derived cell model with iCell cardiomyocytes from 43 normal donors. Several manuscripts detailing the outcomes have been published or are in submission. With these data, we are demonstrating how population Bayesian concentration-response modeling can be used to characterize toxicodynamic (TD) variability and replace the default uncertainty factor for TD variability. Additionally, we demonstrate how this modeling, when combined with high throughput toxicokinetics, can be used to characterize risk through calculation of margins of exposure. We also showed that human iPSC-derived cardiomyocytes are among most informative cell types for rapid hazard characterization of environmental chemicals. Our study showed that human induced pluripotent stem cell (iPSC)-derived cells (hepatocytes, neurons, cardiomyocytes and endothelial cells) and a primary endothelial cell line are a practical high-throughput in vitro model for rapidly evaluating potential hazards of chemicals using a small number of human cells. We demonstrated the potential of this in vitro screening model to inform rapid risk-based decision making through ranking, clustering, and assessment of both hazard and risks of diverse environmental chemicals. Our studies also show that human iPSC-derived cardiomyocytes can be effectively used to study cardiovascular effects of polychlorinated biphenyls and their major metabolites. In a study of 25 PCBs and their major metabolites detected in humans, or in vitro data-based risk characterization analysis showed that while in vitro derived effective concentrations exceed the levels measured in the general population, risks could not be ruled out due to the potential for population variability in susceptibility and the need to fill data gaps using read-across approaches. This study demonstrated a strategy for how in vitro data can be used to characterize human health risks from PCBs and their metabolites. Additional data analyses are under way to process the results of testing 1,000+ compounds selected in consultation with FDA, NTP and EPA in a population-based in vitro iPSC-derived cell model with myCell cardiomyocytes from 5 donors. We also completed collecting samples for whole genome analysis of the effects of drugs and environmental chemicals (650+) on human iPSC-derived cardiomyocytes. These samples have been sent to collaborators at BioSpyder for TempO-seq analysis.
Project 2 investigators continue derivation of iPS from the CC lines. Despite early success in generating robust embryoid bodies from CC derived iPSC, during year 5 most lines continued to lose totipotency, and did not form reproducible embryoid bodies. We were able to address most of the culture issues. We have moved on to culturing the CC derived iPSC we generated and attempted several different differentiation techniques for mass expansion of embryoid bodies. The most promising technology so far is a magnetic spinner flask that keep constant agitation on the embryoid bodies; the speed of agitation controls the size of the embryoid body as well. The first two days of differentiation are the most crucial, therefore this is the part we have been carefully testing and optimizing. Currently we have 4 CC iPSC lines that reproducibly produce embryoid bodies with functional cardiomyocytes. An additional 4 lines are now under developed to match the 8 lines that in vivo cardiotoxicity data has been collected on. To investigate the in vitro-to-in vivo predictive ability of these lines we have increased the number of CC strains to 57 strains that have been used to generate ECG and detailed baseline cardiac phenotypes for CC lines using both male and female mice. A manuscript has been submitted reporting baseline cardiac measures for the CC and new species-specific reference ranges for these cardiac phenotypes, in addition to quantifying the reproducibility of the measures across labs. Concomitant with development of reference ranges, new models of cardiac abnormalities were identified in different CC lines.
Project 3 investigators have refined various aspect of the dose-response pipeline with additional features added, including an area under the curve (AUC) feature, and with additional options to constrain the main Hill model. Various points of departure (POD) have been incorporated, including those based on error variation from controls, or with respect to the underlying fit (as with an effective concentration-based departure). We have also produced code to connect the web version of LocusZoom to SNP mapping results, to better explore the connections between SNP variation and variation in cell-based phenotypes. Down-sampling analyses of TempoSeq data were presented in SOT 2021, and have informed our study designs. We have also developed and implemented a new regression approach to predict multivariate phenotype outcomes from multivariate inputs, such as when high-throughput ‘omics data are used to predict multiple bioassay outcomes in cardiomyocytes simultaneously. The approach has been applied to cardiomyocytes in Luo et al. (2021), and will be implemented for prediction of individual chemical features from the collection of bioassay values, and individual bioassays from the collection of chemical features.
Future Activities:
Project 1 will continue data analysis of the experiments with 5 donors and 1000 chemicals; we will also conduct data analysis for TempO-seq high-throughput transcriptomics on 650+ chemicals in the standard iPSC-cardiomyocyte donor; continue collecting protein binding and other kinetic data to enable in vitro-to-in vivo comparisons; will work closely with Project 3 staff to analyze the data from high-content screening and high-throughput transcriptomics; and will work with project 2 staff to conduct screening of mouse-derived embryoid bodies.
By conclusion of the project, Project 2 anticipates having generated detailed baseline cardiac phenotypes for 57 CC lines, performed genetic analysis to identify the genetic architecture underlying cardiac phenotypic variation, tested 8 iPSC and corresponding isolated cardiomyocytes and CC lines for 4 chemicals identified in Project 1 as candidate cardiotoxicants. Although not of the scale original envisioned, the results will still address the original primary goal of the project: are mice predictive of human cardiotoxicity and do in vitro OCM accurately recapitulate in vivo phenotypes?
Project 3 will release code for the new concentration-response profiling, including simulated annealing maximum likelihood. Additional multivariate penalized regression prediction code will be released in the upcoming year. Analyses of high-throughput data (for example TempOSeq) will occupy much of Project 3 work, using the TempOSeq and bioassay curve-fitting pipelines developed over the past year.
Journal Articles: 44 Displayed | Download in RIS Format
Other center views: | All 149 publications | 44 publications in selected types | All 44 journal articles |
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Auerbach S, Filer D, Reif D, Walker V, Holloway AC, Schlezinger J, Srinivasan S, Svoboda D, Judson R, Bucher JR, Thayer KA. Prioritizing environmental chemicals for obesity and diabetes outcomes research: a screening approach using ToxCastTM high-throughput data. Environmental Health Perspectives 2016;124(8):1141-1154. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) |
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Barton-Maclaren TS, Westphal M, Sarwar E, Mattison D, Chiu WA, Dix D, Kavlock R, Krewski D. Challenges and opportunities in the risk assessment of existing substances in Canada: lessons learned from the international community. International Journal of Risk Assessment and Management 2017;20;(1-3):261-283. |
R835802 (2016) R835802 (2017) R835802 (2018) |
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Blanchette AD, Grimm FA, Dalaijamts C, Hsieh NH, Ferguson K, Luo YS, Anson B, Rusyn I, Chiu WA. Thorough QT/QTc in a dish:An in vitro human model that accurately predicts clinical concentration-QTc relationships. Clinical Pharmacology and Therapeutics 2019;105:1175-1186. |
R835802 (2018) R835802C001 (2018) |
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Blanchette A, Burnett S, Rusyn I, Chiu W. A tiered approach to population-based in vitro testing for cardiotoxicity:Balancing estimates of potency and variability. Journal of Pharmacological and Toxicological Methods 01;119(107154). |
R835802 (2020) |
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Blanchette A, Burnett S, Grimm F, Rusyn I, Chiu W. A Bayesian Method for Population-wide Cardiotoxicity Hazard and Risk Characterization Using an In Vitro Human Model. Toxilogical Sciences 2020;178(2):391-403. |
R835802 (2019) |
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Bokkers BGH, Mengelers MJ, Bakker MI, Chiu WA, Slob W. APROBA-Plus: a probabilistic tool to evaluate and express uncertainty in hazard characterization and exposure assessment of substances. Food and Chemical Toxicology. 2017;110:408-417. |
R835802 (2017) R835802 (2018) |
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Burnett S, Karmakar M, Murphy W, Chiu W, Rusyn I. A new approach method for characterizing inter-species toxicodynamic variability. Journal of Toxicology and Environmental Health, Part A 2021;. |
R835802 (2020) |
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Ceballos D, Luo Y, Chen Z, Blanchette A, Zhou Y, Wright F, Baker E, Chiu W, Rusyn I. Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes. Food and Chemical Toxicology 2021;149:111979. |
R835802 (2019) |
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Chiu WA, Wright FA, Rusyn I. A tiered, Bayesian approach to estimating population variability for regulatory decision-making. ALTEX 2017;34(3):377-388. |
R835802 (2016) R835802 (2017) R835802 (2018) R835166 (2016) R835166 (Final) |
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Chiu WA, Axelrad DA, Dalaijamts C, Dockins C, Shao K, Shapiro AJ, Paoli G. Beyond the RfD:Broad application of a probabilistic approach to improve chemical dose-response assessments for noncancer effects. Environmental Health Perspective 2018;126(6):067009. |
R835802 (2018) R835802C001 (2018) |
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Chiu WA, Guyton KZ, Martin MT, Reif DM, Rusyn I. Use of high-throughput in vitro toxicity screening data in cancer hazard evaluations by IARC Monograph Working Groups. ALTEX 2018;35(1):51-64. |
R835802 (2017) R835802 (2018) R835802C003 (2018) |
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Chiu WA, Rusyn I. Advancing chemical risk assessment decision-making with population variability data: challenges and opportunities. Mammalian Genome 2018;29(1-2):182-189. |
R835802 (2017) R835802 (2018) |
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Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. The next generation of risk assessment multi-year study--highlights of findings, applications to risk assessment, and future directions. Environmental Health Perspectives 2016;124(11):1671-1682. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C001 (2015) R835166 (Final) |
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Fantke P, Aylward L, Bare J, Chiu WA, Dodson R, Dwyer R, Ernstoff A, Howard B, Jantunen M, Jolliet O, Judson R, Kirchhübel N, Li D, Miller A, Paoli G, Price P, Rhomberg L, Shen B, Shin HM, Teeguarden J, Vallero D, Wambaugh J, Wetmore BA, Zaleski R, McKone TE. Advancements in life cycle human exposure and toxicity characterization. Environmetnal Health Perspective 2018;126:125001. |
R835802 (2018) R835802C001 (2018) |
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Garbutt TA, Konneker TI, Konganti K, Hillhouse AE, Swift-Haire F, Jones A, Phelps D, Aylor DL, Threadgill D. Permissiveness to form pluripotent stem cells may be an evolutionarily derived characteristic in Mus musculus. Scientific Reports 2018;8:14706. |
R835802 (2018) R835802C002 (2018) |
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Grimm FA, Iwata Y, Sirenko O, Bittner M, Rusyn I. High-content assay multiplexing for toxicity screening in induced pluripotent stem cell-derived cardiomyocytes and hepatocytes. Assay and Drug Development Technologies 2015;13(9):529-546. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C001 (2015) |
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Grimm FA, Iwata Y, Sirenko O, Chappell GA, Wright FA, Reif DM, Braisted J, Gerhold DL, Yeakley JM, Shepard P, Seligmann B, Roy T, Boogaard PJ, Ketelslegers HB, Rohde AM, Rusyn I. A chemical-biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives. Green Chemistry 2016;18(16):4407-4419. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C001 (2015) R835166 (Final) |
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Grimm FA, Blanchette A, House JS, Ferguson K, Hsieh NH, Dalaijamts C, Wright AA, Anson B, Wright FA, Chiu WA, Rusyn I. A human population-based organotypic in vitro model for cardiotoxicity screening. ALTEX 2018;35:441-452. |
R835802 (2018) R835802C001 (2018) R835802C003 (2018) |
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Grimm FA, House JS, Wilson MR, Sirenko O, Iwata Y, Wright FA, Ball N, Rusyn I. Multi-Dimensional in Vitro Bioactivity Profiling for Grouping of Glycol Ethers. Regulatory Toxicology and Pharmacology 2019;101:91-102. |
R835802 (2018) R835802C001 (2018) R835166 (Final) |
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Grimm FA, Klaren WD, Li X, Lehmler HJ, Karmakar M, Robertson LW, Chiu WA, Rusyn I. Cardiovascular effects of polychlorinated biphenyls and their major metabolites.Environmental Health Perspectives 2020;128(7):077008. |
R835802 (Final) |
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Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. Advancing exposure science through chemical data curation and integration in the Comparative Toxicogenomics Database. Environmental Health Perspectives 2016;124(10):1592-1599. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) |
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Guyton KZ, Rusyn I, Chiu WA, Corpet DE, van den Berg M, Ross MK, Christiani DC, Beland FA, Smith MT. Application of the key characteristics of carcinogens in cancer hazard identification. Carcinogenesis 2018;39(4):614-622. |
R835802 (2017) R835802 (2018) |
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House JS, Grimm FA, Jima DD, Zhou Y-H, Rusyn I, Wright FA. A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics. Frontiers in Genetics 2017;8:168 (11 pp.). |
R835802 (2017) R835802 (2018) |
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Iwata Y, Klaren WD, Lebakken CS, Grimm FA, Rusyn I. High-content assay multiplexing for vascular toxicity screening in induced pluripotent stem cell-derived endothelial cells and human umbilical vein endothelial cells. Assay and Drug Development Technologies 2017;15(6):267-279. |
R835802 (2017) R835802 (2018) R835166 (Final) |
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Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S, Wambaugh J, Woodrow Setzer R, Kothya P, Phuong J, Filer D, Smith D, Reif D, Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS. Editor's highlight: Analysis of the effects of cell stress and cytotoxicity on in vitro assay activity across a diverse chemical and assay space. Toxicological Sciences 2016;152(2):323-339. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) |
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Konganti K, Ehrlich A, Rusyn I, Threadgill DW. gQTL:a web application for QTL analysis using the collaborative cross mouse genetic reference population. G3:Genes, Genomes, Genetics 2018;8(8):2559-2562 |
R835802 (2017) R835802 (2018) R835802C001 (2018) R835802C002 (2018) |
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Li G, Shabalin AA, Rusyn I, Wright FA, Nobel AB. An empirical Bayes approach for multiple tissue eQTL analysis. Biostatistics 2018;19(3):391-406. |
R835802 (2017) R835802 (2018) |
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LInd L, Araujo J, Barchosky A, Belcher S, Berridge B, Chiamvimonvat N, Chiu W, Cogliano V, Elmore S, Farraj A. Key Characteristics of Cardiovascular Toxicants. Environmental Health Perspectives 2021;129(9). |
R835802 (2020) |
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Lu E, Grimm F, Rusyn I, De Saeger S, De Bouvre M, Chiu W. Advancing probabilistic risk assessment by integrating human biomonitoring, new approach methods, and Bayesian modeling:A case study with the mycotoxin deoxynivalenol. ENVIRONMENT INTERNATIONAL 2023;182(108326). |
R835802 (Final) R835166 (Final) |
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Marvel SW, To K, Grimm FA, Wright FA, Rusyn I, Reif DM. ToxPi Graphical User Interface 2.0: dynamic exploration, visualization, and sharing of integrated data models. BMC Bioinformatics 2018;19(1):80 (7 pp.). |
R835802 (2017) R835802 (2018) R835802C001 (2018) R835802C003 (2018) |
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Rusyn I, Greene N. The impact of novel assessment methodologies in toxicology on green chemistry and chemical alternatives. Toxicological Sciences 2018;161(2):276-284. |
R835802 (2017) R835802 (2018) |
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Shah I, Setzer RW, Jack J, Houck KA, Judson RS, Knudsen TB, Liu J, Martin MT, Reif DM, Richard AM, Thomas RS, Crofton KM, Dix DJ, Kavlock RJ. Using ToxCast™ data to reconstruct dynamic cell state trajectories and estimate toxicological points of departure. Environmental Health Perspectives 2016;124(7):910-919. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) |
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Sirenko O, Grimm FA, Ryan KR, Iwata Y, Chiu WA, Parham F, Wignall JA, Anson B, Cromwell EF, Behl M, Rusyn I, Tice RR. In vitro cardiotoxicity assessment of environmental chemicals using an organotypic human induced pluripotent stem cell-derived model. Toxicology and Applied Pharmacology 2017;322:60-74. |
R835802 (2016) R835802 (2017) R835802 (2018) R835166 (Final) |
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Tilley SK, Reif DM, Fry RC. Incorporating ToxCast and Tox21 datasets to rank biological activity of chemicals at Superfund sites in North Carolina. Environment International 2017;101:19-26. |
R835802 (2017) R835802 (2018) |
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Wignall JA, Muratov E, Sedykh A, Guyton KZ, Tropsha A, Rusyn I, Chiu WA. Conditional Toxicity Value (CTV) predictor: an in silico approach for generating quantitative risk estimates for chemicals. Environmental Health Perspectives 2018;126(5):057008 (13 pp.). |
R835802 (2017) R835802 (2018) |
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Zhang G, Marvel S, Truong L, Tanguay RL, Reif DM. Aggregate entropy scoring for quantifying activity across endpoints with irregular correlation structure. Reproductive Toxicology 2016;62:92-99. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) R835168 (Final) R835796 (2017) |
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Zhang G, Roell KR, Truong L, Tanguay RL, Reif DM. A data-driven weighting scheme for multivariate phenotypic endpoints recapitulates zebrafish developmental cascades. Toxicology and Applied Pharmacology 2017;314:109-117. |
R835802 (2016) R835802 (2017) R835802 (2018) R835796 (2017) |
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Zhou Y-H, Marron JS, Wright FA. Computation of ancestry scores with mixed families and unrelated individuals. Biometrics 2018;74(1):155-164. |
R835802 (2016) R835802 (2017) R835802 (2018) |
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Kosnik MB, Strickland JD, Marvel SW, Wallis DJ, Wallace K, Richard AM, Reif DM, Shafer TJ. Concentration–response evaluation of ToxCast compounds for multivariate activity patterns of neural network function. ARCHIVES OF TOXICOLOGY 2013;94:469-484. |
R835802 (2019) |
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Li G, Jima D, Wright FA, Nobel AB. HT-eQTL:integrative expression quantitative trait loci analysis in a large number of human tissues. BMC Bioinformatics 2018;19:95. |
R835802 (2018) R835802C003 (2018) |
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Kosnik MB, Reif DM. Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases. Toxicology and Applied Pharmacology2019;379:114674. |
R835802C003 (2018) |
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Kosnik MB, Planchart A, Marvel SW, Reif DM, Mattingly CJ. Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways. Computational Toxicology2019;12:100094. |
R835802C003 (2018) |
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Chen Z, Liu Y, Wright FA, Chiu WA, Rusyn I. Rapid hazard characterization of environmental chemicals using a compendium of human cell lines from different organs. ALTEX-Alternatives to Animal Experimentation 2020; 37(4):623-638 |
R835802 (2019) |
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Hsieh NH, Reisfeld, B, Bois FY, Chiu WA. Applying a global sensitivity analysis workflow to improve the computational efficiencies in physiologically-based pharmacokinetic modeling. Frontiers in Pharmacology 2018 9:588. |
R835802 (2018) R835802C001 (2018) |
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Progress and Final Reports:
Original Abstract Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
R835802C001 High-throughput Hazard,Dose-responseandPopulationVariabilityAssessmentofCardiotoxicity in aHumanInducedPluripotentStem Cell(iPSC)-derivedinvitro Culture Model
R835802C002 Linking in vitro-to-in vivoToxicity Testing Using
Genetically-matchedOrganoids and Mice from a Novel Genetic Reference Population
R835802C003 A Pipeline for in vitro-to-in vivo Extrapolation, Population Modeling,
& Prioritization
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.
Project Research Results
- Final Report
- 2019 Progress Report
- 2018 Progress Report
- 2017 Progress Report
- 2016 Progress Report
- 2015 Progress Report
- Original Abstract
44 journal articles for this center